Including external shared intel's mkl library in c extension for python

Question

I wrote a python c extension that uses routine from Intel's math kernel library (mkl). This is the first time that I write a c extension. I just learned that today.

The c extension compiled. But when I import it in python, it says undefined symbol, and can't find a function that is defined in the mkl.

How to include any external c library in a python c extension?

Thank you for your help.

mkl_helper.c:

#include "Python.h"
#include "numpy/arrayobject.h"
#include "mkl.h"

static PyObject* test4 (PyObject *self, PyObject *args)
{
    // test4 (m, n,
    //        a, ja, ia,
    //        c, jc, ic)

    PyArrayObject *shape_array;
    PyArrayObject *a_array;   // csr_matrix.data
    PyArrayObject *ja_array;  // csr_matrix.indices
    PyArrayObject *ia_array;  // csr_matrix.indptr
    PyArrayObject *c_array;
    PyArrayObject *jc_array;
    PyArrayObject *ic_array;

    if (!PyArg_ParseTuple(args, "O!O!O!O!O!O!O!", 
                            &PyArray_Type, &shape_array,
                            &PyArray_Type, &a_array,
                            &PyArray_Type, &ja_array,
                            &PyArray_Type, &ia_array,
                            &PyArray_Type, &c_array,
                            &PyArray_Type, &jc_array,
                            &PyArray_Type, &ic_array))
    {
        return NULL;
    }

    long  * ptr_int     = shape_array->data;
    int m               = ptr_int[0];
    int n               = ptr_int[1];
    int k               = n;

    float *  a_data_ptr =  a_array->data;
    float * ja_data_ptr = ja_array->data;
    float * ia_data_ptr = ia_array->data;
    float *  c_data_ptr =  c_array->data;
    float * jc_data_ptr = jc_array->data;
    float * ic_data_ptr = ic_array->data;

    char trans  = 'T';
    int sort    = 0;
    int nzmax   = n*n;
    int info    = -3;
    int request = 0;

    mkl_scsrmultcsr(&trans, &request, &sort,
       &m, &n, &k,
       a_data_ptr, ja_data_ptr, ia_data_ptr,
       a_data_ptr, ja_data_ptr, ia_data_ptr,
       c_data_ptr, jc_data_ptr, ic_data_ptr,
       &nzmax, &info);

    return PyInt_FromLong(info);

}

static struct PyMethodDef methods[] = {
    {"test4", test4, METH_VARARGS, "test2(arr1)\n take a numpy array and return its shape as a tuple"},
    {NULL, NULL, 0, NULL}
};

PyMODINIT_FUNC
initmkl_helper (void)
{
    (void)Py_InitModule("mkl_helper", methods);
    import_array();
}

setup.py:

from distutils.core import setup, Extension
import numpy as np

ext_modules = [ Extension('mkl_helper', sources = ['mkl_helper.c']) ]

setup(
        name = 'mkl_helper',
        version = '1.0',
        include_dirs = [np.get_include()], #Add Include path of numpy
        ext_modules = ext_modules
)

test.py:

import mkl_helper

result of running test.py:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /home/rxu/local/lib/python2.7/site-packages/mkl_helper.so: undefined symbol: mkl_scsrmultcsr

Update 6/16/2016:

this seems to be useful:

1.12. Providing a C API for an Extension Module in https://docs.python.org/2/extending/extending.html says even including one c extension in another c extension can have problems if linked as share library. so, i guess I have to link the mkl as a static library? or add inlcude mkl.h to the python.h?

But then, in python (without c), I can use ctypes.cdll.LoadLibrary("./mkl_rt.so") to load the mkl's shared library and then use c function from the shared library without problem (as in here). Yet Python/C api cannot do the same thing in c?

For linking external c library staticly, the setup.py might need: extra objects in class distutils.core.Extensions at https://docs.python.org/2/distutils/apiref.html?highlight=include#distutils.ccompiler.CCompiler.add_include_dir

Related question about cython with no answer: Combining Cython with MKL

This one seems more helpful: Python, ImportError: undefined symbol: g_utf8_skip

This one use dlopen which is deprecated: Undefined Symbol in C++ When Loading a Python Shared Library

score 1 · Accepted Answer · edited May 23 '17 at 10:29

oopcode's answer in Python, ImportError: undefined symbol: g_utf8_skip works. The situation improved with the following.

importing the c extension into python has no error. Calling the c extension from python give the following error: Intel MKL FATAL ERROR: Cannot load libmkl_mc.so or libmkl_def.so.

I remember when I manually compiled numpy with mkl, the site.cfg file asked for library path and include path for the intel's mkl. Guess I need to add the library path to the extra_link_args as well... But that didn't work.

Someone with anaconda has that error too as in here. Similar case at intel's forum here.

This stackoverflow question says extra_compile_args is also needed: How to pass flag to gcc in Python setup.py script

setup.py

from distutils.core import setup, Extension
import numpy as np

extra_link_args=["-I", "(intel's dir)/intel/compilers_and_libraries_2016.3.210/linux/mkl/include", "-L", "(intel's dir)/intel/mkl/lib/intel64/libmkl_mc.so", "-mkl"] 
ext_modules = [ Extension('mkl_helper', sources = ['mkl_helper.c'], extra_link_args=extra_link_args) ]


setup(
        name = 'mkl_helper',
        version = '1.0',
        include_dirs = [np.get_include()], #Add Include path of numpy
        ext_modules = ext_modules
)

Update: I finally got it working as in here But mkl stillll just use only one of the 12 cpu.

Including external shared intel's mkl library in c extension for python

1 Answers1